is_annotation
type: ObjectProperty
has OBO namespace: ro.obo

is_attribute
type: ObjectProperty
has OBO namespace: ro.obo

is_name
type: ObjectProperty
has OBO namespace: ro.obo

part_of
type: ObjectProperty
type: TransitiveProperty
has OBO namespace: ro.obo

multiple_sequence_alignment
type: Class
has OBO namespace: ro.obo
has related synonym: alignment
has related synonym: msa
has definition: Definition
  label: A representation of a set of sequences, in which structurally or functionally equivalent residues are aligned together. The rows of the multiple alignment represent the different sequences, while the columns represent equivalent residues. Insertions/deletions in the sequences are represented by one or more gap characters.
  has db xref: RO:jt
    type: DbXref
    has URI: http://purl.org/obo/owl/RO#RO_jt

structural_location
type: Class
subclass of: Restriction
  on property: is_attribute
  some values from: amino_acid_residue
has OBO namespace: ro.obo
has definition: The location of the residue in the 3D structure.
  type: Definition
  has db xref: RO:jt
    type: DbXref
    has URI: http://purl.org/obo/owl/RO#RO_jt

residue_function
type: Class
subclass of: Restriction
  on property: is_attribute
  some values from: amino_acid_residue
has OBO namespace: ro.obo
has definition: Function of the residue, such as catalysis, binding or post-translational modification. A residue may exhibit zero, one or more activities.
  type: Definition
  has db xref: RO:jt
    type: DbXref
    has URI: http://purl.org/obo/owl/RO#RO_jt

column_conservation_level
type: Class
subclass of: Restriction
  on property: part_of
  some values from: column_conservation
has OBO namespace: ro.obo
has definition: The level of conservation associated with a given column. This may be specified by either a qualitative score or a quantitative score.
  type: Definition
  has db xref: RO:jt
    type: DbXref
    has URI: http://purl.org/obo/owl/RO#RO_jt

conserved_residue_list
type: Class
subclass of: column_conservation_type
has OBO namespace: ro.obo
has definition: A user specified list of conserved residues.
  type: Definition
  has db xref: RO:jt
    type: DbXref
    has URI: http://purl.org/obo/owl/RO#RO_jt

biological_process
type: Class
subclass of: Restriction
  on property: is_attribute
  some values from: alignment_sequence
has OBO namespace: ro.obo
has definition: GeneOntology interface
  type: Definition
  has db xref: GO:0008150
    type: DbXref
    has URI: http://purl.org/obo/owl/GO#GO_0008150

cellular_component
type: Class
subclass of: Restriction
  on property: is_attribute
  some values from: alignment_sequence
has OBO namespace: ro.obo
has definition: GeneOntology interface
  type: Definition
  has db xref: GO:0005575
    type: DbXref
    has URI: http://purl.org/obo/owl/GO#GO_0005575

molecular_function
type: Class
subclass of: Restriction
  on property: is_attribute
  some values from: alignment_sequence
has OBO namespace: ro.obo
has definition: GeneOntology interface
  type: Definition
  has db xref: GO:0003674
    type: DbXref
    has URI: http://purl.org/obo/owl/GO#GO_0003674

conserved_small_residue
type: Class
subclass of: column_conservation_type
has OBO namespace: ro.obo
has definition: A conserved small residue e.g. PAGST
  type: Definition
  has db xref: RO:jt
    type: DbXref
    has URI: http://purl.org/obo/owl/RO#RO_jt

conserved_negatively_charged_residue
type: Class
subclass of: column_conservation_type
has OBO namespace: ro.obo
has definition: A conserved negatively charged residue e.g. DE
  type: Definition
  has db xref: RO:jt
    type: DbXref
    has URI: http://purl.org/obo/owl/RO#RO_jt

conserved_hydrophobic_residue
type: Class
subclass of: column_conservation_type
has OBO namespace: ro.obo
has definition: A conserved hydrophobic residue e.g. ACFGLIMVWY
  type: Definition
  has db xref: RO:jt
    type: DbXref
    has URI: http://purl.org/obo/owl/RO#RO_jt

conserved_hydrophilic_residue
type: Class
subclass of: column_conservation_type
has OBO namespace: ro.obo
has definition: A conserved hydrophilic residue e.g. DEHKNQRST
  type: Definition
  has db xref: RO:jt
    type: DbXref
    has URI: http://purl.org/obo/owl/RO#RO_jt

quantitative_conservation_level
type: Class
subclass of: column_conservation_level
has OBO namespace: ro.obo
has definition: A quantitative score for the conservation associated with a given column.
  type: Definition
  has db xref: RO:jt
    type: DbXref
    has URI: http://purl.org/obo/owl/RO#RO_jt

qualitative_conservation_level
type: Class
subclass of: column_conservation_level
has OBO namespace: ro.obo
has definition: A qualitative description of the level of conservation associated with a given column.
  type: Definition
  has db xref: RO:jt
    type: DbXref
    has URI: http://purl.org/obo/owl/RO#RO_jt

low_conservation
type: Class
subclass of: qualitative_conservation_level
has OBO namespace: ro.obo
has definition: A low level of conservation associated with a given column.
  type: Definition
  has db xref: RO:jt
    type: DbXref
    has URI: http://purl.org/obo/owl/RO#RO_jt

medium_conservation
type: Class
subclass of: qualitative_conservation_level
has OBO namespace: ro.obo
has definition: A medium level of conservation associated with a given column.
  type: Definition
  has db xref: RO:jt
    type: DbXref
    has URI: http://purl.org/obo/owl/RO#RO_jt

high_conservation
type: Class
subclass of: qualitative_conservation_level
has OBO namespace: ro.obo
has definition: A high level of conservation associated with a given column.
  type: Definition
  has db xref: RO:jt
    type: DbXref
    has URI: http://purl.org/obo/owl/RO#RO_jt

catalytic_site
type: Class
subclass of: enzyme_active_site
has OBO namespace: ro.obo
has definition: A residue that is directly involved in some aspect of the reaction catalysed by the enzyme.
  type: Definition
  has db xref: RO:jt
    type: DbXref
    has URI: http://purl.org/obo/owl/RO#RO_jt

domain
type: Class
subclass of: sequence_feature_type
has OBO namespace: ro.obo
has definition: Definition
  label: A discrete portion of a protein assumed to fold independently of the rest of the protein and possessing its own function. [NCBI Bioinformatics] A region of a proteins amino acid sequence that has evolutionary, structural, or functional significance. The amino acid sequence of a domain determines a proteins 3D structure. [CHI Structural proteomics report]
  has db xref: RO:jt
    type: DbXref
    has URI: http://purl.org/obo/owl/RO#RO_jt

post_translational_modification
type: Class
subclass of: residue_function
has OBO namespace: ro.obo
has related synonym: ptm
has definition: Definition
  label: A sequence modification that occurs after synthesis of the protein on the ribosome. e.g. cleavage (thus eliminating signal sequences, transit or pro- peptides and initiator methionines) or addition of simple chemical groups or more complex molecules, such as sugars and lipids. (Human Proteomics Initiative) http://www.expasy.ch/sprot/hpi/ n
  has db xref: RO:jt
    type: DbXref
    has URI: http://purl.org/obo/owl/RO#RO_jt

psi_mutation
type: Class
subclass of: mutation
has OBO namespace: ro.obo
has definition: PSI interface
  type: Definition
  has db xref: MI:0118
    type: DbXref
    has URI: http://purl.org/obo/owl/MI#MI_0118

msa_construction_method
type: Class
subclass of: Restriction
  on property: is_annotation
  some values from: multiple_sequence_alignment
has OBO namespace: ro.obo
has definition: The method used to construct the multiple sequence alignment.
  type: Definition
  has db xref: RO:jt
    type: DbXref
    has URI: http://purl.org/obo/owl/RO#RO_jt

3d_atomic_point
type: Class
subclass of: Restriction
  on property: is_attribute
  some values from: atom
has OBO namespace: ro.obo
has definition: The x,y,z coordinates of the atom in 3-dimensional space.
  type: Definition
  has db xref: RO:jt
    type: DbXref
    has URI: http://purl.org/obo/owl/RO#RO_jt

N_terminal
type: Class
subclass of: structural_location
has OBO namespace: ro.obo
has related synonym: amino_terminus
has definition: A residue in a protein chain that has a free amino group.
  type: Definition
  has db xref: RO:jt
    type: DbXref
    has URI: http://purl.org/obo/owl/RO#RO_jt

C_terminal
type: Class
subclass of: structural_location
has OBO namespace: ro.obo
has related synonym: carboxyl_terminus
has definition: A residue in a protein chain that has a free carboxyl group.
  type: Definition
  has db xref: RO:jt
    type: DbXref
    has URI: http://purl.org/obo/owl/RO#RO_jt

in_domain
type: Class
subclass of: structural_location
has OBO namespace: ro.obo
has definition: A residue in a domain i.e. in a discrete portion of a protein assumed to fold independently of the rest of the protein and possessing its own function. [NCBI Bioinformatics]
  type: Definition
  has db xref: RO:jt
    type: DbXref
    has URI: http://purl.org/obo/owl/RO#RO_jt

in_hinge_region
type: Class
subclass of: structural_location
has OBO namespace: ro.obo
has definition: A residue in a hinge region i.e. a flexible region of the protein between two globular domains.
  type: Definition
  has db xref: RO:jt
    type: DbXref
    has URI: http://purl.org/obo/owl/RO#RO_jt

in_transmembrane_region
type: Class
subclass of: structural_location
has OBO namespace: ro.obo
has definition: Definition
  label: A residue in a transmembrane region i.e. in a domain in a amphipathic membrane protein where the hydrophobic regions traverse the lipid bilayers of the membranes, while the hydrophilic regions extend on either side of the membrane and interact with water.[Folding@home glossary, Stanford Univ].
  has db xref: RO:jt
    type: DbXref
    has URI: http://purl.org/obo/owl/RO#RO_jt

in_helix
type: Class
subclass of: structural_location
has OBO namespace: ro.obo
has definition: Definition
  label: A residue in a helical portion of a protein structure i.e. in a frequently highly stable protein chain conformation stabilised by hydrogen bonding between peptide groups and having side chains projecting outwards in a spiral (3.6 residues per turn). [The Biochemical Society Glossary].
  has db xref: RO:jt
    type: DbXref
    has URI: http://purl.org/obo/owl/RO#RO_jt

in_strand
type: Class
subclass of: structural_location
has OBO namespace: ro.obo
has definition: A residue in a beta_strand i.e. a stable
has related synonym: in_beta_strand

in_loop
type: Class
subclass of: structural_location
has OBO namespace: ro.obo
has definition: A residue in a loop i.e. a section of the protein chain connecting classical secondary structures like helix and sheet. [The Biochemical Society Glossary].
  type: Definition
  has db xref: RO:jt
    type: DbXref
    has URI: http://purl.org/obo/owl/RO#RO_jt

sub_alignment
type: Class
subclass of: Restriction
  on property: part_of
  some values from: multiple_sequence_alignment
has OBO namespace: ro.obo
has definition: A subset of sequences in the msa. e.g. a phylogenetic subgroup such as 'mammals', or a sequence cluster calculated by an automatic method such as secator/dpc or any other subset.
  type: Definition
  has db xref: RO:jt
    type: DbXref
    has URI: http://purl.org/obo/owl/RO#RO_jt
has related synonym: sub_group
has related synonym: cluster
has related synonym: group

residue
type: Class
subclass of: Restriction
  on property: part_of
  some values from: alignment_sequence
subclass of: Restriction
  on property: part_of
  some values from: alignment_column
has OBO namespace: ro.obo
has definition: Definition
  label: The part of a single sugar that appears in a polysaccharide; of a single amino acid in a protein; of a single nucleotide in a nucleic acid, etc.; usually the monomer minus the elements of water.Glossary of Biochemistry and Molecular Biology, David M. Glick.
  has db xref: RO:jt
    type: DbXref
    has URI: http://purl.org/obo/owl/RO#RO_jt

gap_character
type: Class
subclass of: Restriction
  on property: part_of
  some values from: alignment_column
subclass of: Restriction
  on property: part_of
  some values from: alignment_sequence
has OBO namespace: ro.obo
has definition: The character used to represent an insertion/deletion.
  type: Definition
  has db xref: RO:jt
    type: DbXref
    has URI: http://purl.org/obo/owl/RO#RO_jt

unknown_residue_function
type: Class
subclass of: residue_function
has OBO namespace: ro.obo

unknown_structural_location
type: Class
subclass of: structural_location
has OBO namespace: ro.obo

kegg_id
type: Class
subclass of: Restriction
  on property: is_attribute
  some values from: alignment_sequence
has OBO namespace: ro.obo
has definition: KEGG interface
  type: Definition
  has db xref: KEGG:xref
    type: DbXref
    has URI: http://purl.org/obo/owl/KEGG#KEGG_xref

alignment_sequence
type: Class
subclass of: Restriction
  on property: part_of
  some values from: sub_alignment
has OBO namespace: ro.obo
has related synonym: sequence
has definition: The order of residues and insertions/deletions represented by gap characters in a single sequence. For proteins, this is known as the primary structure.
  type: Definition
  has db xref: RO:jt
    type: DbXref
    has URI: http://purl.org/obo/owl/RO#RO_jt

sequence_name
type: Class
subclass of: Restriction
  on property: is_name
  some values from: alignment_sequence
has OBO namespace: ro.obo
has related synonym: seq_name
has definition: The name given to the sequence.
  type: Definition
  has db xref: RO:jt
    type: DbXref
    has URI: http://purl.org/obo/owl/RO#RO_jt

column_score
type: Class
subclass of: Restriction
  on property: is_attribute
  some values from: alignment_column
has OBO namespace: ro.obo
has definition: A score associated with a given column.
  type: Definition
  has db xref: RO:jt
    type: DbXref
    has URI: http://purl.org/obo/owl/RO#RO_jt

column_conservation_type
type: Class
subclass of: Restriction
  on property: part_of
  some values from: column_conservation
has OBO namespace: ro.obo
has definition: The type of residue conserved in a given column.
  type: Definition
  has db xref: RO:jt
    type: DbXref
    has URI: http://purl.org/obo/owl/RO#RO_jt

organism
type: Class
subclass of: Restriction
  on property: is_attribute
  some values from: alignment_sequence
has OBO namespace: ro.obo
has definition: The organism that was the source of the sequence.
  type: Definition
  has db xref: RO:jt
    type: DbXref
    has URI: http://purl.org/obo/owl/RO#RO_jt

sequence_feature
type: Class
subclass of: Restriction
  on property: is_attribute
  some values from: alignment_sequence
has OBO namespace: ro.obo
has related synonym: fitem
has definition: A region of the sequence, defined by a start and stop residue, that has a specific property.
  type: Definition
  has db xref: RO:jt
    type: DbXref
    has URI: http://purl.org/obo/owl/RO#RO_jt

feature_start_residue
type: Class
subclass of: Restriction
  on property: part_of
  some values from: sequence_feature
has OBO namespace: ro.obo
has definition: The residue at the beginning of the feature.
  type: Definition
  has db xref: RO:jt
    type: DbXref
    has URI: http://purl.org/obo/owl/RO#RO_jt
has related synonym: fstart

feature_stop_residue
type: Class
subclass of: Restriction
  on property: part_of
  some values from: sequence_feature
has OBO namespace: ro.obo
has related synonym: fstop
has definition: The residue at the end of the feature.
  type: Definition
  has db xref: RO:jt
    type: DbXref
    has URI: http://purl.org/obo/owl/RO#RO_jt

consensus_sequence
type: Class
subclass of: Restriction
  on property: part_of
  some values from: sub_alignment
has OBO namespace: ro.obo
has definition: A pseudo-sequence that summarises the residue information contained in an aligned set of sequences.
  type: Definition
  has db xref: RO:jt
    type: DbXref
    has URI: http://purl.org/obo/owl/RO#RO_jt

column_weight
type: Class
subclass of: Restriction
  on property: is_attribute
  some values from: alignment_column
has OBO namespace: ro.obo
has definition: A weight associated with a given column.
  type: Definition
  has db xref: RO:jt
    type: DbXref
    has URI: http://purl.org/obo/owl/RO#RO_jt

sequence_weight
type: Class
subclass of: Restriction
  on property: is_attribute
  some values from: alignment_sequence
has OBO namespace: ro.obo
has definition: A weight assigned to a sequence.
  type: Definition
  has db xref: RO:jt
    type: DbXref
    has URI: http://purl.org/obo/owl/RO#RO_jt
has related synonym: weight

feature_description
type: Class
subclass of: Restriction
  on property: part_of
  some values from: sequence_feature
has OBO namespace: ro.obo
has definition: A general text description of the feature.
  type: Definition
  has db xref: RO:jt
    type: DbXref
    has URI: http://purl.org/obo/owl/RO#RO_jt
has related synonym: fnote

protein:protein interactions
type: Class
subclass of: residue_function
has OBO namespace: ro.obo
has definition: PSI interface
  type: Definition
  has db xref: MI:0000
    type: DbXref
    has URI: http://purl.org/obo/owl/MI#MI_0000

msa_name
type: Class
subclass of: Restriction
  on property: is_name
  some values from: multiple_sequence_alignment
has OBO namespace: ro.obo
has related synonym: aln_name
has definition: The name given to the multiple sequence alignment.
  type: Definition
  has db xref: RO:jt
    type: DbXref
    has URI: http://purl.org/obo/owl/RO#RO_jt

ec_number
type: Class
subclass of: Restriction
  on property: is_attribute
  some values from: alignment_sequence
has OBO namespace: ro.obo
has related synonym: ec
has definition: Enzyme Commission interface
  type: Definition
  has db xref: EC:xref
    type: DbXref
    has URI: http://purl.org/obo/owl/EC#EC_xref

hydrophobicity
type: Class
subclass of: Restriction
  on property: is_attribute
  some values from: alignment_sequence
has OBO namespace: ro.obo
has definition: A measure of how insoluble a given molecule is when in water or other polar liquids.
  type: Definition
  has db xref: RO:jt
    type: DbXref
    has URI: http://purl.org/obo/owl/RO#RO_jt

feature_name
type: Class
subclass of: Restriction
  on property: is_name
  some values from: sequence_feature
has OBO namespace: ro.obo
has definition: The name given to the feature.
  type: Definition
  has db xref: RO:jt
    type: DbXref
    has URI: http://purl.org/obo/owl/RO#RO_jt

sequence_feature_type
type: Class
subclass of: Restriction
  on property: part_of
  some values from: sequence_feature
has OBO namespace: ro.obo
has related synonym: ftype
has definition: The type of the sequence feature.
  type: Definition
  has db xref: RO:jt
    type: DbXref
    has URI: http://purl.org/obo/owl/RO#RO_jt

interpro_domain
type: Class
subclass of: domain
has OBO namespace: ro.obo
has definition: Interpro interface
  type: Definition
  has db xref: IPR:xref
    type: DbXref
    has URI: http://purl.org/obo/owl/IPR#IPR_xref

transmembrane_helix
type: Class
subclass of: residue_hydrogen_bond
has OBO namespace: ro.obo
has related synonym: tm

coiled_coil
type: Class
subclass of: sequence_feature_type
has OBO namespace: ro.obo

msa_core_block
type: Class
subclass of: sequence_feature_type
has OBO namespace: ro.obo
has definition: A conserved region in the sub_alignment.
  type: Definition
  has db xref: RO:jt
    type: DbXref
    has URI: http://purl.org/obo/owl/RO#RO_jt

helix
type: Class
subclass of: sequence_feature_type
has OBO namespace: ro.obo
has narrow synonym: alpha_helix
has definition: Definition
  label: A frequently highly stable protein chain conformation stabilised by hydrogen bonding between peptide groups and having side chains projecting outwards in a spiral (3.6 residues per turn). The Biochemical Society Glossary.
  has db xref: RO:jt
    type: DbXref
    has URI: http://purl.org/obo/owl/RO#RO_jt

strand
type: Class
subclass of: sequence_feature_type
has OBO namespace: ro.obo
has definition: Stable
has related synonym: beta_strand

accession_number
type: Class
subclass of: Restriction
  on property: is_attribute
  some values from: alignment_sequence
has OBO namespace: ro.obo
has definition: A unique identifier in the sequence databases.Accession numbers should remain static between database updates.
  type: Definition
  has db xref: RO:jt
    type: DbXref
    has URI: http://purl.org/obo/owl/RO#RO_jt
has related synonym: accession

sequence_description
type: Class
subclass of: Restriction
  on property: is_attribute
  some values from: alignment_sequence
has OBO namespace: ro.obo
has definition: A general description of the sequence.
  type: Definition
  has db xref: RO:jt
    type: DbXref
    has URI: http://purl.org/obo/owl/RO#RO_jt

taxid
type: Class
subclass of: Restriction
  on property: is_attribute
  some values from: alignment_sequence
has OBO namespace: ro.obo
has definition: NCBI taxonomy database interface
  type: Definition
  has db xref: taxid:xref
    type: DbXref
    has URI: http://purl.org/obo/owl/taxid#taxid_xref

sequence_repeat
type: Class
subclass of: sequence_feature_type
has OBO namespace: ro.obo
has definition: A region which has multiple copies in the sequence. Repeats range from short stretches of adjacent, similar residues to multiple copies of complete domains.
  type: Definition
  has db xref: RO:jt
    type: DbXref
    has URI: http://purl.org/obo/owl/RO#RO_jt

signal
type: Class
subclass of: sequence_feature_type
has OBO namespace: ro.obo
has definition: Extent of a signal sequence (prepeptide).
  type: Definition
  has db xref: RO:jt
    type: DbXref
    has URI: http://purl.org/obo/owl/RO#RO_jt

sequence_variant
type: Class
subclass of: sequence_feature_type
has OBO namespace: ro.obo
has definition: A region where an alternative sequence has been observed.
  type: Definition
  has db xref: RO:jt
    type: DbXref
    has URI: http://purl.org/obo/owl/RO#RO_jt
has related synonym: varsplic

low_complexity_region
type: Class
subclass of: sequence_feature_type
has OBO namespace: ro.obo
has definition: Definition
  label: A region of biased residue composition, e.g. homopolymeric runs, short repeats, and more subtle overrepresentations of one or a few residues. Low-complexity regions in amino acid sequences typically assume non-globular structure in proteins. [NCBI sef.glossary).
  has db xref: RO:jt
    type: DbXref
    has URI: http://purl.org/obo/owl/RO#RO_jt

site
type: Class
subclass of: sequence_feature_type
has OBO namespace: ro.obo
has definition: A generic term for the extent of a user-specified site.
  type: Definition
  has db xref: RO:jt
    type: DbXref
    has URI: http://purl.org/obo/owl/RO#RO_jt

sequence_keyword_list
type: Class
subclass of: Restriction
  on property: is_attribute
  some values from: alignment_sequence
has OBO namespace: ro.obo
has definition: A list of keywords that provide information that can be used to generate indexes of the sequence entries based on functional, structural, or other categories.
  type: Definition
  has db xref: RO:jt
    type: DbXref
    has URI: http://purl.org/obo/owl/RO#RO_jt

buried
type: Class
subclass of: structural_location
has OBO namespace: ro.obo
has definition: A residue in the core of the protein that has no surface area accessible to solvent.
  type: Definition
  has db xref: RO:jt
    type: DbXref
    has URI: http://purl.org/obo/owl/RO#RO_jt
has related synonym: core_residue

residue_hydrogen_bond
type: Class
subclass of: residue_structural_bond
has OBO namespace: ro.obo
has definition: A type of attractive intermolecular force that exists between two partial electric charges of opposite polarity.
  type: Definition
  has db xref: RO:jt
    type: DbXref
    has URI: http://purl.org/obo/owl/RO#RO_jt

conserved_aliphatic_residue
type: Class
subclass of: column_conservation_type
has OBO namespace: ro.obo
has definition: A conserved aliphatic residue e.g. AGLIV
  type: Definition
  has db xref: RO:jt
    type: DbXref
    has URI: http://purl.org/obo/owl/RO#RO_jt

conserved_aromatic_residue
type: Class
subclass of: column_conservation_type
has OBO namespace: ro.obo
has definition: A conserved aromatic residue e.g. YWFH
  type: Definition
  has db xref: RO:jt
    type: DbXref
    has URI: http://purl.org/obo/owl/RO#RO_jt

conserved_basic_residue
type: Class
subclass of: column_conservation_type
has OBO namespace: ro.obo
has definition: A conserved basic residue e.g. HKR
  type: Definition
  has db xref: RO:jt
    type: DbXref
    has URI: http://purl.org/obo/owl/RO#RO_jt

conserved_hydroxyl_residue
type: Class
subclass of: column_conservation_type
has OBO namespace: ro.obo
has definition: A conserved hydroxyl residue e.g. STY
  type: Definition
  has db xref: RO:jt
    type: DbXref
    has URI: http://purl.org/obo/owl/RO#RO_jt

dna_binding_site
type: Class
subclass of: residue_function
has OBO namespace: ro.obo
has definition: A residue that is directly involved in binding to dna.
  type: Definition
  has db xref: RO:jt
    type: DbXref
    has URI: http://purl.org/obo/owl/RO#RO_jt

column_conservation
type: Class
subclass of: Restriction
  on property: is_attribute
  some values from: alignment_column
has OBO namespace: ro.obo
has definition: The conservation associated with a given column in the msa.
  type: Definition
  has db xref: RO:jt
    type: DbXref
    has URI: http://purl.org/obo/owl/RO#RO_jt

residue_function_detection_method
type: Class
subclass of: Restriction
  on property: is_annotation
  some values from: residue_function
has OBO namespace: ro.obo
has definition: The method used to detect the activity or function of the residue.
  type: Definition
  has db xref: RO:jt
    type: DbXref
    has URI: http://purl.org/obo/owl/RO#RO_jt

column_conservation_construction_method
type: Class
subclass of: Restriction
  on property: is_annotation
  some values from: column_conservation
has OBO namespace: ro.obo
has definition: The method used to construct the conservation score associated with a given column.
  type: Definition
  has db xref: RO:jt
    type: DbXref
    has URI: http://purl.org/obo/owl/RO#RO_jt

user_conservation_value
type: Class
subclass of: qualitative_conservation_level
has OBO namespace: ro.obo
has definition: A user defined conservation term e.g. mixed conservation from different methods
  type: Definition
  has db xref: RO:jt
    type: DbXref
    has URI: http://purl.org/obo/owl/RO#RO_jt

strict_conservation
type: Class
subclass of: qualitative_conservation_level
has OBO namespace: ro.obo
has definition: A strictly conserved column.
  type: Definition
  has db xref: RO:jt
    type: DbXref
    has URI: http://purl.org/obo/owl/RO#RO_jt

no_conservation
type: Class
subclass of: qualitative_conservation_level
has OBO namespace: ro.obo
has definition: An unconserved column.
  type: Definition
  has db xref: RO:jt
    type: DbXref
    has URI: http://purl.org/obo/owl/RO#RO_jt

in_cavity
type: Class
subclass of: structural_location
has OBO namespace: ro.obo
has related synonym: in_pocket
has definition: The residue is touching a cavity.
  type: Definition
  has db xref: RO:pk
    type: DbXref
    has URI: http://purl.org/obo/owl/RO#RO_pk

alignment_column
type: Class
subclass of: Restriction
  on property: part_of
  some values from: sub_alignment
has OBO namespace: ro.obo
has definition: Definition
  label: The alignment_column contains one residue (or a gap character) from each sequence. The residues in the column are considered to be equivalent. If no equivalent residue exists for a given sequence, a gap character is inserted.
  has db xref: RO:jt
    type: DbXref
    has URI: http://purl.org/obo/owl/RO#RO_jt

sub_alignment_construction_method
type: Class
subclass of: Restriction
  on property: is_annotation
  some values from: sub_alignment
has OBO namespace: ro.obo
has related synonym: sub_group_construction_method
has definition: The method used to determine the sub_alignment or sub_families.
  type: Definition
  has db xref: RO:jt
    type: DbXref
    has URI: http://purl.org/obo/owl/RO#RO_jt
has related synonym: cluster_construction_method
has related synonym: group_construction_method

loop
type: Class
subclass of: sequence_feature_type
has OBO namespace: ro.obo
has definition: Definition
  label: A section of the protein chain connecting classical secondary structures like helix and sheet. Often of irregular structure, surface exposed and containing hydrophilic residues. The Biochemical Society Glossary.
  has db xref: RO:jt
    type: DbXref
    has URI: http://purl.org/obo/owl/RO#RO_jt

group
type: Class
subclass of: alignment_sequence
has OBO namespace: ro.obo
has definition: The group or cluster the sequence belongs to.
  type: Definition
  has db xref: RO:jt
    type: DbXref
    has URI: http://purl.org/obo/owl/RO#RO_jt
has related synonym: cluster

feature_score
type: Class
subclass of: Restriction
  on property: part_of
  some values from: sequence_feature
has OBO namespace: ro.obo
has related synonym: fscore
has definition: A score associated with the feature.
  type: Definition
  has db xref: RO:jt
    type: DbXref
    has URI: http://purl.org/obo/owl/RO#RO_jt

feature_color
type: Class
subclass of: Restriction
  on property: part_of
  some values from: sequence_feature
has OBO namespace: ro.obo
has related synonym: fcolour
has related synonym: feature_colour
has definition: A color used to display the feature.
  type: Definition
  has db xref: RO:jt
    type: DbXref
    has URI: http://purl.org/obo/owl/RO#RO_jt
has related synonym: fcolor

differential_conservation
type: Class
subclass of: qualitative_conservation_level
has OBO namespace: ro.obo
has definition: A column that is conserved differently in the different sub_families. e.g. a residue that is conserved in mammals, but is divergent in the other organisms.
  type: Definition
  has db xref: RO:jt
    type: DbXref
    has URI: http://purl.org/obo/owl/RO#RO_jt

conserved_gap_character
type: Class
subclass of: column_conservation_type
has OBO namespace: ro.obo
has definition: A conserved insertion/deletion.
  type: Definition
  has db xref: RO:jt
    type: DbXref
    has URI: http://purl.org/obo/owl/RO#RO_jt

structural_location_detection_method
type: Class
subclass of: Restriction
  on property: is_annotation
  some values from: structural_location
has OBO namespace: ro.obo
has definition: The method used to determine the location of the residue in the 3d structure.
  type: Definition
  has db xref: RO:jt
    type: DbXref
    has URI: http://purl.org/obo/owl/RO#RO_jt

3d_atomic_coordinate
type: Class
subclass of: Restriction
  on property: part_of
  some values from: 3d_atomic_point
has OBO namespace: ro.obo
has definition: The coordinate of the atom in 3-dimensional space.
  type: Definition
  has db xref: RO:jt
    type: DbXref
    has URI: http://purl.org/obo/owl/RO#RO_jt

atom
type: Class
subclass of: Restriction
  on property: part_of
  some values from: nucleotide_residue
subclass of: Restriction
  on property: part_of
  some values from: amino_acid_residue
has OBO namespace: ro.obo
has definition: The fundamental building blocks of chemistry, which cannot be broken by any chemical means.
  type: Definition
  has db xref: RO:jt
    type: DbXref
    has URI: http://purl.org/obo/owl/RO#RO_jt

other_residue_function
type: Class
subclass of: residue_function
has OBO namespace: ro.obo
has definition: A user specified activity or function associated with a residue.
  type: Definition
  has db xref: RO:jt
    type: DbXref
    has URI: http://purl.org/obo/owl/RO#RO_jt

pdb_name
type: Class
subclass of: Restriction
  on property: is_attribute
  some values from: alignment_sequence
has OBO namespace: ro.obo

msa_3d_superposition
type: Class
subclass of: Restriction
  on property: is_attribute
  some values from: alignment_sequence
has OBO namespace: ro.obo

msa_reference_structure_name
type: Class
subclass of: Restriction
  on property: part_of
  some values from: msa_3d_superposition
has OBO namespace: ro.obo

msa_superposed_regions
type: Class
subclass of: Restriction
  on property: part_of
  some values from: msa_3d_superposition
has OBO namespace: ro.obo

msa_symmetry_operator
type: Class
subclass of: Restriction
  on property: part_of
  some values from: msa_3d_superposition
has OBO namespace: ro.obo

msa_rmsd
type: Class
subclass of: Restriction
  on property: part_of
  some values from: msa_3d_superposition
has OBO namespace: ro.obo

tissue_type
type: Class
subclass of: Restriction
  on property: is_attribute
  some values from: alignment_sequence
has OBO namespace: ro.obo
has definition: The tissue from which the sequence was extracted.
  type: Definition
  has db xref: RO:jt
    type: DbXref
    has URI: http://purl.org/obo/owl/RO#RO_jt

developmental_stage
type: Class
subclass of: Restriction
  on property: is_attribute
  some values from: alignment_sequence
has OBO namespace: ro.obo
has definition: The developmental stage of the organism's life cycle during which the sequence was extracted nMGED Interface
  type: Definition
  has db xref: RO:jt
    type: DbXref
    has URI: http://purl.org/obo/owl/RO#RO_jt

exposed
type: Class
subclass of: structural_location
has OBO namespace: ro.obo
has related synonym: surface_residue
has definition: A residue on the surface of the protein that is accessible to solvent.
  type: Definition
  has db xref: RO:jt
    type: DbXref
    has URI: http://purl.org/obo/owl/RO#RO_jt

residue_salt_bridge
type: Class
subclass of: residue_structural_bond
has OBO namespace: ro.obo
has definition: An interaction between positive and negative charges on side chains of a protein.
  type: Definition
  has db xref: RO:jt
    type: DbXref
    has URI: http://purl.org/obo/owl/RO#RO_jt

ramachandran_plot
type: Class
subclass of: Restriction
  on property: is_attribute
  some values from: amino_acid_residue
has OBO namespace: ro.obo
has definition: The Ramachandran plot is a graph of the protein backbone torsional angles psi (Calpha-C bond) versus phi (N-Calpha bond). The psi and phi angles cover the ranges from -180 to +1800.
  type: Definition
  has db xref: RO:pk
    type: DbXref
    has URI: http://purl.org/obo/owl/RO#RO_pk

phi_angle
type: Class
subclass of: ramachandran_plot
has OBO namespace: ro.obo
has definition: The phi (N-Calpha bond) protein backbone torsional angles of the Ramachandran plot. The phi angle cover the range from -180 to +1800.
  type: Definition
  has db xref: RO:pk
    type: DbXref
    has URI: http://purl.org/obo/owl/RO#RO_pk

3d_coordinate_x
type: Class
subclass of: 3d_atomic_coordinate
has OBO namespace: ro.obo

psi_angle
type: Class
subclass of: ramachandran_plot
has OBO namespace: ro.obo
has definition: The psi (C-Calpha bond) protein backbone torsional angles of the Ramachandran plot. The phi angle cover the range from -180 to +1800.
  type: Definition
  has db xref: RO:pk
    type: DbXref
    has URI: http://purl.org/obo/owl/RO#RO_pk

3d_coordinate_y
type: Class
subclass of: 3d_atomic_coordinate
has OBO namespace: ro.obo

3d_coordinate_z
type: Class
subclass of: 3d_atomic_coordinate
has OBO namespace: ro.obo

bonded_residue
type: Class
subclass of: Restriction
  on property: is_attribute
  some values from: residue_structural_bond
has OBO namespace: ro.obo
has definition: The other residue bonded to the reference residue.
  type: Definition
  has db xref: RO:jt
    type: DbXref
    has URI: http://purl.org/obo/owl/RO#RO_jt

msa_freetext_line
type: Class
subclass of: Restriction
  on property: part_of
  some values from: sub_alignment
has OBO namespace: ro.obo
has definition: A line of free text in the msa, containing annotation associated with a sequence or group of sequences.
  type: Definition
  has db xref: RO:jt
    type: DbXref
    has URI: http://purl.org/obo/owl/RO#RO_jt
has related synonym: aln_text

msa_freetext_owner
type: Class
subclass of: Restriction
  on property: is_attribute
  some values from: msa_freetext_line
has OBO namespace: ro.obo
has definition: The alignment_sequence or sub_family that the msa_freetext is attached to.
  type: Definition
  has db xref: RO:jt
    type: DbXref
    has URI: http://purl.org/obo/owl/RO#RO_jt
has related synonym: aln_text_owner

msa_freetext_type
type: Class
subclass of: Restriction
  on property: is_attribute
  some values from: msa_freetext_line
has OBO namespace: ro.obo
has definition: The type of text supplied in the msa_freetext.
  type: Definition
  has db xref: RO:jt
    type: DbXref
    has URI: http://purl.org/obo/owl/RO#RO_jt
has related synonym: aln_text_type

consensus_sequence_construction_method
type: Class
subclass of: Restriction
  on property: is_annotation
  some values from: consensus_sequence
has OBO namespace: ro.obo
has definition: The method used to determine the consensus sequence.
  type: Definition
  has db xref: RO:jt
    type: DbXref
    has URI: http://purl.org/obo/owl/RO#RO_jt

sequence_type
type: Class
subclass of: Restriction
  on property: is_attribute
  some values from: alignment_sequence
has OBO namespace: ro.obo
has definition: The type of sequence e.g. protein or dna.
  type: Definition
  has db xref: RO:jt
    type: DbXref
    has URI: http://purl.org/obo/owl/RO#RO_jt

column_score_calculation_method
type: Class
subclass of: Restriction
  on property: is_annotation
  some values from: column_score
has OBO namespace: ro.obo
has definition: The method used to calculate the score associated with a given column.
  type: Definition
  has db xref: RO:jt
    type: DbXref
    has URI: http://purl.org/obo/owl/RO#RO_jt

column_weight_calculation_method
type: Class
subclass of: Restriction
  on property: is_annotation
  some values from: alignment_column
has OBO namespace: ro.obo
has definition: The method used to calculate the weight associated with a given column.
  type: Definition
  has db xref: RO:jt
    type: DbXref
    has URI: http://purl.org/obo/owl/RO#RO_jt

amino_acid_residue
type: Class
subclass of: residue
has OBO namespace: ro.obo
has related synonym: amino_acid
has related synonym: aa_residue
has related synonym: aa
has definition: An organic compound that generally contains an amino (-NH2) and a carboxyl (-COOH) group. There are 20 different kinds of amino acids. A protein consists of a specific sequence of amino acids.
  type: Definition
  has db xref: RO:jt
    type: DbXref
    has URI: http://purl.org/obo/owl/RO#RO_jt

nucleotide_residue
type: Class
subclass of: residue
has OBO namespace: ro.obo
has definition: A DNA sequence consists of a specific sequence of nucleotides. A nucleotide is made of a molecule of sugar, a molecule of phosphoric acid, and a molecule called a base. The bases are the
has related synonym: nucleotide
has related synonym: base_pair
has related synonym: base

atom_name
type: Class
subclass of: Restriction
  on property: is_name
  some values from: atom
has OBO namespace: ro.obo

motif
type: Class
subclass of: sequence_feature_type
has OBO namespace: ro.obo
has definition: A pattern of conserved residues in a sequence that are located within a certain distance from each other in the sequence.
  type: Definition
  has db xref: RO:jt
    type: DbXref
    has URI: http://purl.org/obo/owl/RO#RO_jt

enzyme_active_site
type: Class
subclass of: residue_function
has OBO namespace: ro.obo
has definition: Definition
  label: The active site of an enzyme is the binding site where catalysis occurs. The structure and chemical properties of the active site allow the recognition and binding of the substrate. The active site consists of the catalytic amino acids and one or more binding sites that bind the substrate(s).
  has db xref: RO:jt
    type: DbXref
    has URI: http://purl.org/obo/owl/RO#RO_jt

substrate_binding_site
type: Class
subclass of: enzyme_active_site
has OBO namespace: ro.obo
has definition: A residue that is directly involved in the binding of a specific substrate.
  type: Definition
  has db xref: RO:jt
    type: DbXref
    has URI: http://purl.org/obo/owl/RO#RO_jt

mutation
type: Class
subclass of: residue_function
has OBO namespace: ro.obo
has definition: A mutation is a permanent, transmissible change to the genetic material (usually DNA or RNA) of a cell.
  type: Definition
  has db xref: RO:jt
    type: DbXref
    has URI: http://purl.org/obo/owl/RO#RO_jt

point_mutation
type: Class
subclass of: mutation
has OBO namespace: ro.obo
has definition: Definition
  label: A point mutation is usually caused by chemicals or malfunction of DNA replication and exchanges a single nucleotide for another. Most common is the transition that exchanges a purine for a purine or a pyrimidine for a pyrimidine (A ? G, C ? T). Less common is a transversion, which exchanges a purine for a pyrimidine or a pyrimidine for a purine (C/T ? A/G).
  has db xref: RO:jt
    type: DbXref
    has URI: http://purl.org/obo/owl/RO#RO_jt

insertion_mutation
type: Class
subclass of: mutation
has OBO namespace: ro.obo
has definition: Definition
  label: The addition of one or more extra nucleotides into the DNA. They are usually caused by transposable elements, or errors during replication of repeating elements (e.g. AT repeats). Insertions in a gene can cause a shift in the reading frame (frameshift) or alter splicing of the mRNA, both of which can significantly alter the gene product.
  has db xref: RO:jt
    type: DbXref
    has URI: http://purl.org/obo/owl/RO#RO_jt

deletion_mutation
type: Class
subclass of: mutation
has OBO namespace: ro.obo
has definition: Definition
  label: Deletions remove one or more nucleotides from the DNA. Like insertions, these mutations can alter the reading frame of the gene. Deletions in a gene can cause a shift in the reading frame (frameshift) or alter splicing of the mRNA, both of which can significantly alter the gene product.
  has db xref: RO:jt
    type: DbXref
    has URI: http://purl.org/obo/owl/RO#RO_jt

silent_mutation
type: Class
subclass of: point_mutation
has OBO namespace: ro.obo
has definition: Definition
  label: A silent mutation is a DNA mutation that does not alter the final amino acid, and hence does not affect the final protein. Anaylsis of mutations in genes causing genetic disorders has shown that silent mutations can affect gene transcription, leading to the formation of truncated protein with reduced or no function.
  has db xref: RO:jt
    type: DbXref
    has URI: http://purl.org/obo/owl/RO#RO_jt
has related synonym: synonymous_mutation

missense_mutation
type: Class
subclass of: point_mutation
has OBO namespace: ro.obo
has definition: A missense mutations is a type of point mutation where a nucleotide is changed which results in a different amino acid. This in turn can render the resulting protein nonfunctional.
  type: Definition
  has db xref: RO:jt
    type: DbXref
    has URI: http://purl.org/obo/owl/RO#RO_jt
has related synonym: nonsynonymous_mutation

nonsense_mutation
type: Class
subclass of: point_mutation
has OBO namespace: ro.obo
has definition: A nonsense mutation is a point mutation that results in a premature stop codon in the transcribed mRNA, and possibly a truncated (and often nonfunctional) protein product.
  type: Definition
  has db xref: RO:jt
    type: DbXref
    has URI: http://purl.org/obo/owl/RO#RO_jt

mutation_type
type: Class
subclass of: Restriction
  on property: is_attribute
  some values from: mutation
has OBO namespace: ro.obo
has definition: The type fo mutation. e.g. germline mutation, which can be passed on to progeny or somatic mutation, which often leads to the malfunction or death of a cell and can cause cancer.
  type: Definition
  has db xref: RO:jt
    type: DbXref
    has URI: http://purl.org/obo/owl/RO#RO_jt

metal_binding_site
type: Class
subclass of: ligand_binding_site
has OBO namespace: ro.obo
has definition: A residue that is directly involved in the binding of a metal ion.
  type: Definition
  has db xref: RO:jt
    type: DbXref
    has URI: http://purl.org/obo/owl/RO#RO_jt

CSA_catalytic_site
type: Class
subclass of: catalytic_site
has OBO namespace: ro.obo
has definition: CSA Interface
  type: Definition
  has db xref: RO:jt
    type: DbXref
    has URI: http://purl.org/obo/owl/RO#RO_jt

ligand_binding_site
type: Class
subclass of: residue_function
has OBO namespace: ro.obo
has definition: A residue that is directly involved in the binding of a specific ligand.
  type: Definition
  has db xref: RO:jt
    type: DbXref
    has URI: http://purl.org/obo/owl/RO#RO_jt

mutation_phenotypic_manifestation
type: Class
subclass of: Restriction
  on property: is_attribute
  some values from: mutation
has OBO namespace: ro.obo
has definition: OBO_phenotype_ontology interface
  type: Definition
  has db xref: RO:jt
    type: DbXref
    has URI: http://purl.org/obo/owl/RO#RO_jt

resid_ptm
type: Class
subclass of: post_translational_modification
has OBO namespace: ro.obo
has definition: RESID database interface
  type: Definition
  has db xref: RO:jt
    type: DbXref
    has URI: http://purl.org/obo/owl/RO#RO_jt

acetylation
type: Class
subclass of: post_translational_modification
has OBO namespace: ro.obo
has definition: N-terminal of some residues and side chain of lysine or cysteine
  type: Definition
  has db xref: RO:jt
    type: DbXref
    has URI: http://purl.org/obo/owl/RO#RO_jt

amidation
type: Class
subclass of: post_translational_modification
has OBO namespace: ro.obo
has definition: Generally at the C-terminal of a mature active peptide after oxidative cleavage of last glycine
  type: Definition
  has db xref: RO:jt
    type: DbXref
    has URI: http://purl.org/obo/owl/RO#RO_jt

blocked
type: Class
subclass of: post_translational_modification
has OBO namespace: ro.obo
has definition: Unidentified N- or C-terminal blocking group
  type: Definition
  has db xref: RO:jt
    type: DbXref
    has URI: http://purl.org/obo/owl/RO#RO_jt

formylation
type: Class
subclass of: post_translational_modification
has OBO namespace: ro.obo
has definition: Of the N-terminal methionine
  type: Definition
  has db xref: RO:jt
    type: DbXref
    has URI: http://purl.org/obo/owl/RO#RO_jt

gamma_carboygluamic_acid
type: Class
subclass of: post_translational_modification
has OBO namespace: ro.obo
has definition: Of glutamate
  type: Definition
  has db xref: RO:jt
    type: DbXref
    has URI: http://purl.org/obo/owl/RO#RO_jt

hydroxylation
type: Class
subclass of: post_translational_modification
has OBO namespace: ro.obo
has definition: Generally of asparagine, aspartate, proline or lysine
  type: Definition
  has db xref: RO:jt
    type: DbXref
    has URI: http://purl.org/obo/owl/RO#RO_jt

methylation
type: Class
subclass of: post_translational_modification
has OBO namespace: ro.obo
has definition: Generally of N-terminal phenylalanine, side chain of lysine, arginine, histidine, asparagine or glutamate, and C-terminal cysteine
  type: Definition
  has db xref: RO:jt
    type: DbXref
    has URI: http://purl.org/obo/owl/RO#RO_jt

phosphorylation
type: Class
subclass of: post_translational_modification
has OBO namespace: ro.obo
has definition: Of serine, threonine, tyrosine, aspartate, histidine or cysteine
  type: Definition
  has db xref: RO:jt
    type: DbXref
    has URI: http://purl.org/obo/owl/RO#RO_jt

pyrrolidone_carboxylic_acid
type: Class
subclass of: post_translational_modification
has OBO namespace: ro.obo
has definition: N-terminal glutamine which has formed an internal cyclic lactam. This is also called 'pyro-Glu'. Very rarely, pyro-Glu can be produced by modification of a N-terminal glutamate
  type: Definition
  has db xref: RO:jt
    type: DbXref
    has URI: http://purl.org/obo/owl/RO#RO_jt

sulfation
type: Class
subclass of: post_translational_modification
has OBO namespace: ro.obo
has definition: Of tyrosine, serine or threonine
  type: Definition
  has db xref: RO:jt
    type: DbXref
    has URI: http://purl.org/obo/owl/RO#RO_jt

carbohydrate_binding_site
type: Class
subclass of: ligand_binding_site
has OBO namespace: ro.obo

lipid_binding_site
type: Class
subclass of: ligand_binding_site
has OBO namespace: ro.obo
has definition: A residue that is directly involved in the binding of a lipid.
  type: Definition
  has db xref: RO:jt
    type: DbXref
    has URI: http://purl.org/obo/owl/RO#RO_jt

residue_disulfide_bond
type: Class
subclass of: residue_structural_bond
has OBO namespace: ro.obo
has definition: A strong covalent bond between two sulfhydryl groups. This bond is very important to the folding, structure, and function of proteins.
  type: Definition
  has db xref: RO:jt
    type: DbXref
    has URI: http://purl.org/obo/owl/RO#RO_jt
has related synonym: disulfide_bridge

residue_structural_bond
type: Class
subclass of: residue_function
has OBO namespace: ro.obo

sequence_length
type: Class
subclass of: Restriction
  on property: is_attribute
  some values from: alignment_sequence
has OBO namespace: ro.obo
has related synonym: length
has definition: The length of the sequence.
  type: Definition
  has db xref: RO:jt
    type: DbXref
    has URI: http://purl.org/obo/owl/RO#RO_jt

n_terminal_extension
type: Class
subclass of: sequence_feature_type
has OBO namespace: ro.obo

c_terminal_extension
type: Class
subclass of: sequence_feature_type
has OBO namespace: ro.obo

sequence_weight_calculation_method
type: Class
subclass of: Restriction
  on property: is_annotation
  some values from: sequence_weight
has OBO namespace: ro.obo

sequence_insertion
type: Class
subclass of: sequence_feature_type
has OBO namespace: ro.obo

column_consensus
type: Class
subclass of: Restriction
  on property: is_attribute
  some values from: alignment_column
has OBO namespace: ro.obo
has definition: A consensus character that summarises the residue information contained in an alignment_column.
  type: Definition
  has db xref: RO:jt
    type: DbXref
    has URI: http://purl.org/obo/owl/RO#RO_jt

feature_calculation_method
type: Class
subclass of: Restriction
  on property: is_annotation
  some values from: sequence_feature
has OBO namespace: ro.obo
has definition: The method used to determine the feature.
  type: Definition
  has db xref: RO:jt
    type: DbXref
    has URI: http://purl.org/obo/owl/RO#RO_jt

column_consensus_calculation_method
type: Class
subclass of: Restriction
  on property: is_annotation
  some values from: column_consensus
has OBO namespace: ro.obo
has definition: The method used to determine the consensus character associated with a column.
  type: Definition
  has db xref: RO:jt
    type: DbXref
    has URI: http://purl.org/obo/owl/RO#RO_jt

so_mutation
type: Class
subclass of: mutation
has OBO namespace: ro.obo
has definition: SO interface
  type: Definition
  has db xref: RO:jt
    type: DbXref
    has URI: http://purl.org/obo/owl/RO#RO_jt

sequence_keyword
type: Class
subclass of: Restriction
  on property: part_of
  some values from: sequence_keyword_list
has OBO namespace: ro.obo
has definition: A keyword provides information that can be used to generate indexes of the sequence entries based on functional, structural, or other categories.
  type: Definition
  has db xref: RO:jt
    type: DbXref
    has URI: http://purl.org/obo/owl/RO#RO_jt

hydrophobicity_calculation_method
type: Class
subclass of: Restriction
  on property: is_annotation
  some values from: hydrophobicity
has OBO namespace: ro.obo
has definition: The method used to calculate the hydrophobicity measure.
  type: Definition
  has db xref: RO:jt
    type: DbXref
    has URI: http://purl.org/obo/owl/RO#RO_jt